- static {\r
- hydrophobic.put("I",new Integer(1));\r
- hydrophobic.put("L",new Integer(1));\r
- hydrophobic.put("V",new Integer(1));\r
- hydrophobic.put("C",new Integer(1));\r
- hydrophobic.put("A",new Integer(1));\r
- hydrophobic.put("G",new Integer(1));\r
- hydrophobic.put("M",new Integer(1));\r
- hydrophobic.put("F",new Integer(1));\r
- hydrophobic.put("Y",new Integer(1));\r
- hydrophobic.put("W",new Integer(1));\r
- hydrophobic.put("H",new Integer(1));\r
- hydrophobic.put("K",new Integer(1));\r
- hydrophobic.put("X",new Integer(1));\r
- hydrophobic.put("-",new Integer(1));\r
- hydrophobic.put("*",new Integer(1));\r
- hydrophobic.put("R",new Integer(0));\r
- hydrophobic.put("E",new Integer(0));\r
- hydrophobic.put("Q",new Integer(0));\r
- hydrophobic.put("D",new Integer(0));\r
- hydrophobic.put("N",new Integer(0));\r
- hydrophobic.put("S",new Integer(0));\r
- hydrophobic.put("T",new Integer(0));\r
- hydrophobic.put("P",new Integer(0));\r
- }\r
- static {\r
- polar.put("Y",new Integer(1));\r
- polar.put("W",new Integer(1));\r
- polar.put("H",new Integer(1));\r
- polar.put("K",new Integer(1));\r
- polar.put("R",new Integer(1));\r
- polar.put("E",new Integer(1));\r
- polar.put("Q",new Integer(1));\r
- polar.put("D",new Integer(1));\r
- polar.put("N",new Integer(1));\r
- polar.put("S",new Integer(1));\r
- polar.put("T",new Integer(1));\r
- polar.put("X",new Integer(1));\r
- polar.put("-",new Integer(1));\r
- polar.put("*",new Integer(1));\r
- polar.put("I",new Integer(0));\r
- polar.put("L",new Integer(0));\r
- polar.put("V",new Integer(0));\r
- polar.put("C",new Integer(0));\r
- polar.put("A",new Integer(0));\r
- polar.put("G",new Integer(0));\r
- polar.put("M",new Integer(0));\r
- polar.put("F",new Integer(0));\r
- polar.put("P",new Integer(0));\r
-\r
- }\r
- static {\r
- small.put("I",new Integer(0));\r
- small.put("L",new Integer(0));\r
- small.put("V",new Integer(1));\r
- small.put("C",new Integer(1));\r
- small.put("A",new Integer(1));\r
- small.put("G",new Integer(1));\r
- small.put("M",new Integer(0));\r
- small.put("F",new Integer(0));\r
- small.put("Y",new Integer(0));\r
- small.put("W",new Integer(0));\r
- small.put("H",new Integer(0));\r
- small.put("K",new Integer(0));\r
- small.put("R",new Integer(0));\r
- small.put("E",new Integer(0));\r
- small.put("Q",new Integer(0));\r
- small.put("D",new Integer(1));\r
- small.put("N",new Integer(1));\r
- small.put("S",new Integer(1));\r
- small.put("T",new Integer(1));\r
- small.put("P",new Integer(1));\r
- small.put("-",new Integer(1));\r
- small.put("*",new Integer(1));\r
- }\r
- static {\r
- positive.put("I",new Integer(0));\r
- positive.put("L",new Integer(0));\r
- positive.put("V",new Integer(0));\r
- positive.put("C",new Integer(0));\r
- positive.put("A",new Integer(0));\r
- positive.put("G",new Integer(0));\r
- positive.put("M",new Integer(0));\r
- positive.put("F",new Integer(0));\r
- positive.put("Y",new Integer(0));\r
- positive.put("W",new Integer(0));\r
- positive.put("H",new Integer(1));\r
- positive.put("K",new Integer(1));\r
- positive.put("R",new Integer(1));\r
- positive.put("E",new Integer(0));\r
- positive.put("Q",new Integer(0));\r
- positive.put("D",new Integer(0));\r
- positive.put("N",new Integer(0));\r
- positive.put("S",new Integer(0));\r
- positive.put("T",new Integer(0));\r
- positive.put("P",new Integer(0));\r
- positive.put("-",new Integer(1));\r
- positive.put("*",new Integer(1));\r
- }\r
- static {\r
- negative.put("I",new Integer(0));\r
- negative.put("L",new Integer(0));\r
- negative.put("V",new Integer(0));\r
- negative.put("C",new Integer(0));\r
- negative.put("A",new Integer(0));\r
- negative.put("G",new Integer(0));\r
- negative.put("M",new Integer(0));\r
- negative.put("F",new Integer(0));\r
- negative.put("Y",new Integer(0));\r
- negative.put("W",new Integer(0));\r
- negative.put("H",new Integer(0));\r
- negative.put("K",new Integer(0));\r
- negative.put("R",new Integer(0));\r
- negative.put("E",new Integer(1));\r
- negative.put("Q",new Integer(0));\r
- negative.put("D",new Integer(1));\r
- negative.put("N",new Integer(0));\r
- negative.put("S",new Integer(0));\r
- negative.put("T",new Integer(0));\r
- negative.put("P",new Integer(0));\r
- negative.put("-",new Integer(1));\r
- negative.put("*",new Integer(1));\r
- }\r
- static {\r
- charged.put("I",new Integer(0));\r
- charged.put("L",new Integer(0));\r
- charged.put("V",new Integer(0));\r
- charged.put("C",new Integer(0));\r
- charged.put("A",new Integer(0));\r
- charged.put("G",new Integer(0));\r
- charged.put("M",new Integer(0));\r
- charged.put("F",new Integer(0));\r
- charged.put("Y",new Integer(0));\r
- charged.put("W",new Integer(0));\r
- charged.put("H",new Integer(1));\r
- charged.put("K",new Integer(1));\r
- charged.put("R",new Integer(1));\r
- charged.put("E",new Integer(1));\r
- charged.put("Q",new Integer(0));\r
- charged.put("D",new Integer(1));\r
- charged.put("N",new Integer(1));\r
- charged.put("S",new Integer(0));\r
- charged.put("T",new Integer(0));\r
- charged.put("P",new Integer(0));\r
- charged.put("-",new Integer(1));\r
- charged.put("*",new Integer(1));\r
- }\r
- static {\r
- aromatic.put("I",new Integer(0));\r
- aromatic.put("L",new Integer(0));\r
- aromatic.put("V",new Integer(0));\r
- aromatic.put("C",new Integer(0));\r
- aromatic.put("A",new Integer(0));\r
- aromatic.put("G",new Integer(0));\r
- aromatic.put("M",new Integer(0));\r
- aromatic.put("F",new Integer(1));\r
- aromatic.put("Y",new Integer(1));\r
- aromatic.put("W",new Integer(1));\r
- aromatic.put("H",new Integer(1));\r
- aromatic.put("K",new Integer(0));\r
- aromatic.put("R",new Integer(0));\r
- aromatic.put("E",new Integer(0));\r
- aromatic.put("Q",new Integer(0));\r
- aromatic.put("D",new Integer(0));\r
- aromatic.put("N",new Integer(0));\r
- aromatic.put("S",new Integer(0));\r
- aromatic.put("T",new Integer(0));\r
- aromatic.put("P",new Integer(0));\r
- aromatic.put("-",new Integer(1));\r
- aromatic.put("*",new Integer(1));\r
- }\r
- static {\r
- aliphatic.put("I",new Integer(1));\r
- aliphatic.put("L",new Integer(1));\r
- aliphatic.put("V",new Integer(1));\r
- aliphatic.put("C",new Integer(0));\r
- aliphatic.put("A",new Integer(0));\r
- aliphatic.put("G",new Integer(0));\r
- aliphatic.put("M",new Integer(0));\r
- aliphatic.put("F",new Integer(0));\r
- aliphatic.put("Y",new Integer(0));\r
- aliphatic.put("W",new Integer(0));\r
- aliphatic.put("H",new Integer(0));\r
- aliphatic.put("K",new Integer(0));\r
- aliphatic.put("R",new Integer(0));\r
- aliphatic.put("E",new Integer(0));\r
- aliphatic.put("Q",new Integer(0));\r
- aliphatic.put("D",new Integer(0));\r
- aliphatic.put("N",new Integer(0));\r
- aliphatic.put("S",new Integer(0));\r
- aliphatic.put("T",new Integer(0));\r
- aliphatic.put("P",new Integer(0));\r
- aliphatic.put("-",new Integer(1));\r
- aliphatic.put("*",new Integer(1));\r
- }\r
-\r
- static {\r
- tiny.put("I",new Integer(0));\r
- tiny.put("L",new Integer(0));\r
- tiny.put("V",new Integer(0));\r
- tiny.put("C",new Integer(0));\r
- tiny.put("A",new Integer(1));\r
- tiny.put("G",new Integer(1));\r
- tiny.put("M",new Integer(0));\r
- tiny.put("F",new Integer(0));\r
- tiny.put("Y",new Integer(0));\r
- tiny.put("W",new Integer(0));\r
- tiny.put("H",new Integer(0));\r
- tiny.put("K",new Integer(0));\r
- tiny.put("R",new Integer(0));\r
- tiny.put("E",new Integer(0));\r
- tiny.put("Q",new Integer(0));\r
- tiny.put("D",new Integer(0));\r
- tiny.put("N",new Integer(0));\r
- tiny.put("S",new Integer(1));\r
- tiny.put("T",new Integer(0));\r
- tiny.put("P",new Integer(0));\r
- tiny.put("-",new Integer(1));\r
- tiny.put("*",new Integer(1));\r
- }\r
-\r
- static {\r
- proline.put("I",new Integer(0));\r
- proline.put("L",new Integer(0));\r
- proline.put("V",new Integer(0));\r
- proline.put("C",new Integer(0));\r
- proline.put("A",new Integer(0));\r
- proline.put("G",new Integer(0));\r
- proline.put("M",new Integer(0));\r
- proline.put("F",new Integer(0));\r
- proline.put("Y",new Integer(0));\r
- proline.put("W",new Integer(0));\r
- proline.put("H",new Integer(0));\r
- proline.put("K",new Integer(0));\r
- proline.put("R",new Integer(0));\r
- proline.put("E",new Integer(0));\r
- proline.put("Q",new Integer(0));\r
- proline.put("D",new Integer(0));\r
- proline.put("N",new Integer(0));\r
- proline.put("S",new Integer(0));\r
- proline.put("T",new Integer(0));\r
- proline.put("P",new Integer(1));\r
- proline.put("-",new Integer(1));\r
- proline.put("*",new Integer(1));\r
- }\r
-\r
-\r
- static {\r
- propHash.put("hydrophobic",hydrophobic);\r
- propHash.put("small",small);\r
- propHash.put("positive",positive);\r
- propHash.put("negative",negative);\r
- propHash.put("charged",charged);\r
- propHash.put("aromatic",aromatic);\r
- propHash.put("aliphatic",aliphatic);\r
- propHash.put("tiny",tiny);\r
- propHash.put("proline",proline);\r
- propHash.put("polar",polar);\r
- }\r
-\r
- public static Hashtable chainColours = new Hashtable();\r
- static {\r
- chainColours.put("A",Color.red);\r
- chainColours.put("B",Color.orange);\r
- chainColours.put("C",Color.yellow);\r
- chainColours.put("D",Color.green);\r
- chainColours.put("E",Color.cyan);\r
- chainColours.put("F",Color.blue);\r
- chainColours.put("G",Color.magenta);\r
- chainColours.put("H",Color.pink);\r
- }\r
- public static Hashtable getChainColours() {\r
- return chainColours;\r
+ static\r
+ {\r
+ hydrophobic.put("I", new Integer(1));\r
+ hydrophobic.put("L", new Integer(1));\r
+ hydrophobic.put("V", new Integer(1));\r
+ hydrophobic.put("C", new Integer(1));\r
+ hydrophobic.put("A", new Integer(1));\r
+ hydrophobic.put("G", new Integer(1));\r
+ hydrophobic.put("M", new Integer(1));\r
+ hydrophobic.put("F", new Integer(1));\r
+ hydrophobic.put("Y", new Integer(1));\r
+ hydrophobic.put("W", new Integer(1));\r
+ hydrophobic.put("H", new Integer(1));\r
+ hydrophobic.put("K", new Integer(1));\r
+ hydrophobic.put("X", new Integer(1));\r
+ hydrophobic.put("-", new Integer(1));\r
+ hydrophobic.put("*", new Integer(1));\r
+ hydrophobic.put("R", new Integer(0));\r
+ hydrophobic.put("E", new Integer(0));\r
+ hydrophobic.put("Q", new Integer(0));\r
+ hydrophobic.put("D", new Integer(0));\r
+ hydrophobic.put("N", new Integer(0));\r
+ hydrophobic.put("S", new Integer(0));\r
+ hydrophobic.put("T", new Integer(0));\r
+ hydrophobic.put("P", new Integer(0));\r
+ }\r
+\r
+ static\r
+ {\r
+ polar.put("Y", new Integer(1));\r
+ polar.put("W", new Integer(1));\r
+ polar.put("H", new Integer(1));\r
+ polar.put("K", new Integer(1));\r
+ polar.put("R", new Integer(1));\r
+ polar.put("E", new Integer(1));\r
+ polar.put("Q", new Integer(1));\r
+ polar.put("D", new Integer(1));\r
+ polar.put("N", new Integer(1));\r
+ polar.put("S", new Integer(1));\r
+ polar.put("T", new Integer(1));\r
+ polar.put("X", new Integer(1));\r
+ polar.put("-", new Integer(1));\r
+ polar.put("*", new Integer(1));\r
+ polar.put("I", new Integer(0));\r
+ polar.put("L", new Integer(0));\r
+ polar.put("V", new Integer(0));\r
+ polar.put("C", new Integer(0));\r
+ polar.put("A", new Integer(0));\r
+ polar.put("G", new Integer(0));\r
+ polar.put("M", new Integer(0));\r
+ polar.put("F", new Integer(0));\r
+ polar.put("P", new Integer(0));\r
+ }\r
+\r
+ static\r
+ {\r
+ small.put("I", new Integer(0));\r
+ small.put("L", new Integer(0));\r
+ small.put("V", new Integer(1));\r
+ small.put("C", new Integer(1));\r
+ small.put("A", new Integer(1));\r
+ small.put("G", new Integer(1));\r
+ small.put("M", new Integer(0));\r
+ small.put("F", new Integer(0));\r
+ small.put("Y", new Integer(0));\r
+ small.put("W", new Integer(0));\r
+ small.put("H", new Integer(0));\r
+ small.put("K", new Integer(0));\r
+ small.put("R", new Integer(0));\r
+ small.put("E", new Integer(0));\r
+ small.put("Q", new Integer(0));\r
+ small.put("D", new Integer(1));\r
+ small.put("N", new Integer(1));\r
+ small.put("S", new Integer(1));\r
+ small.put("T", new Integer(1));\r
+ small.put("P", new Integer(1));\r
+ small.put("-", new Integer(1));\r
+ small.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ positive.put("I", new Integer(0));\r
+ positive.put("L", new Integer(0));\r
+ positive.put("V", new Integer(0));\r
+ positive.put("C", new Integer(0));\r
+ positive.put("A", new Integer(0));\r
+ positive.put("G", new Integer(0));\r
+ positive.put("M", new Integer(0));\r
+ positive.put("F", new Integer(0));\r
+ positive.put("Y", new Integer(0));\r
+ positive.put("W", new Integer(0));\r
+ positive.put("H", new Integer(1));\r
+ positive.put("K", new Integer(1));\r
+ positive.put("R", new Integer(1));\r
+ positive.put("E", new Integer(0));\r
+ positive.put("Q", new Integer(0));\r
+ positive.put("D", new Integer(0));\r
+ positive.put("N", new Integer(0));\r
+ positive.put("S", new Integer(0));\r
+ positive.put("T", new Integer(0));\r
+ positive.put("P", new Integer(0));\r
+ positive.put("-", new Integer(1));\r
+ positive.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ negative.put("I", new Integer(0));\r
+ negative.put("L", new Integer(0));\r
+ negative.put("V", new Integer(0));\r
+ negative.put("C", new Integer(0));\r
+ negative.put("A", new Integer(0));\r
+ negative.put("G", new Integer(0));\r
+ negative.put("M", new Integer(0));\r
+ negative.put("F", new Integer(0));\r
+ negative.put("Y", new Integer(0));\r
+ negative.put("W", new Integer(0));\r
+ negative.put("H", new Integer(0));\r
+ negative.put("K", new Integer(0));\r
+ negative.put("R", new Integer(0));\r
+ negative.put("E", new Integer(1));\r
+ negative.put("Q", new Integer(0));\r
+ negative.put("D", new Integer(1));\r
+ negative.put("N", new Integer(0));\r
+ negative.put("S", new Integer(0));\r
+ negative.put("T", new Integer(0));\r
+ negative.put("P", new Integer(0));\r
+ negative.put("-", new Integer(1));\r
+ negative.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ charged.put("I", new Integer(0));\r
+ charged.put("L", new Integer(0));\r
+ charged.put("V", new Integer(0));\r
+ charged.put("C", new Integer(0));\r
+ charged.put("A", new Integer(0));\r
+ charged.put("G", new Integer(0));\r
+ charged.put("M", new Integer(0));\r
+ charged.put("F", new Integer(0));\r
+ charged.put("Y", new Integer(0));\r
+ charged.put("W", new Integer(0));\r
+ charged.put("H", new Integer(1));\r
+ charged.put("K", new Integer(1));\r
+ charged.put("R", new Integer(1));\r
+ charged.put("E", new Integer(1));\r
+ charged.put("Q", new Integer(0));\r
+ charged.put("D", new Integer(1));\r
+ charged.put("N", new Integer(1));\r
+ charged.put("S", new Integer(0));\r
+ charged.put("T", new Integer(0));\r
+ charged.put("P", new Integer(0));\r
+ charged.put("-", new Integer(1));\r
+ charged.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ aromatic.put("I", new Integer(0));\r
+ aromatic.put("L", new Integer(0));\r
+ aromatic.put("V", new Integer(0));\r
+ aromatic.put("C", new Integer(0));\r
+ aromatic.put("A", new Integer(0));\r
+ aromatic.put("G", new Integer(0));\r
+ aromatic.put("M", new Integer(0));\r
+ aromatic.put("F", new Integer(1));\r
+ aromatic.put("Y", new Integer(1));\r
+ aromatic.put("W", new Integer(1));\r
+ aromatic.put("H", new Integer(1));\r
+ aromatic.put("K", new Integer(0));\r
+ aromatic.put("R", new Integer(0));\r
+ aromatic.put("E", new Integer(0));\r
+ aromatic.put("Q", new Integer(0));\r
+ aromatic.put("D", new Integer(0));\r
+ aromatic.put("N", new Integer(0));\r
+ aromatic.put("S", new Integer(0));\r
+ aromatic.put("T", new Integer(0));\r
+ aromatic.put("P", new Integer(0));\r
+ aromatic.put("-", new Integer(1));\r
+ aromatic.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ aliphatic.put("I", new Integer(1));\r
+ aliphatic.put("L", new Integer(1));\r
+ aliphatic.put("V", new Integer(1));\r
+ aliphatic.put("C", new Integer(0));\r
+ aliphatic.put("A", new Integer(0));\r
+ aliphatic.put("G", new Integer(0));\r
+ aliphatic.put("M", new Integer(0));\r
+ aliphatic.put("F", new Integer(0));\r
+ aliphatic.put("Y", new Integer(0));\r
+ aliphatic.put("W", new Integer(0));\r
+ aliphatic.put("H", new Integer(0));\r
+ aliphatic.put("K", new Integer(0));\r
+ aliphatic.put("R", new Integer(0));\r
+ aliphatic.put("E", new Integer(0));\r
+ aliphatic.put("Q", new Integer(0));\r
+ aliphatic.put("D", new Integer(0));\r
+ aliphatic.put("N", new Integer(0));\r
+ aliphatic.put("S", new Integer(0));\r
+ aliphatic.put("T", new Integer(0));\r
+ aliphatic.put("P", new Integer(0));\r
+ aliphatic.put("-", new Integer(1));\r
+ aliphatic.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ tiny.put("I", new Integer(0));\r
+ tiny.put("L", new Integer(0));\r
+ tiny.put("V", new Integer(0));\r
+ tiny.put("C", new Integer(0));\r
+ tiny.put("A", new Integer(1));\r
+ tiny.put("G", new Integer(1));\r
+ tiny.put("M", new Integer(0));\r
+ tiny.put("F", new Integer(0));\r
+ tiny.put("Y", new Integer(0));\r
+ tiny.put("W", new Integer(0));\r
+ tiny.put("H", new Integer(0));\r
+ tiny.put("K", new Integer(0));\r
+ tiny.put("R", new Integer(0));\r
+ tiny.put("E", new Integer(0));\r
+ tiny.put("Q", new Integer(0));\r
+ tiny.put("D", new Integer(0));\r
+ tiny.put("N", new Integer(0));\r
+ tiny.put("S", new Integer(1));\r
+ tiny.put("T", new Integer(0));\r
+ tiny.put("P", new Integer(0));\r
+ tiny.put("-", new Integer(1));\r
+ tiny.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ proline.put("I", new Integer(0));\r
+ proline.put("L", new Integer(0));\r
+ proline.put("V", new Integer(0));\r
+ proline.put("C", new Integer(0));\r
+ proline.put("A", new Integer(0));\r
+ proline.put("G", new Integer(0));\r
+ proline.put("M", new Integer(0));\r
+ proline.put("F", new Integer(0));\r
+ proline.put("Y", new Integer(0));\r
+ proline.put("W", new Integer(0));\r
+ proline.put("H", new Integer(0));\r
+ proline.put("K", new Integer(0));\r
+ proline.put("R", new Integer(0));\r
+ proline.put("E", new Integer(0));\r
+ proline.put("Q", new Integer(0));\r
+ proline.put("D", new Integer(0));\r
+ proline.put("N", new Integer(0));\r
+ proline.put("S", new Integer(0));\r
+ proline.put("T", new Integer(0));\r
+ proline.put("P", new Integer(1));\r
+ proline.put("-", new Integer(1));\r
+ proline.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ propHash.put("hydrophobic", hydrophobic);\r
+ propHash.put("small", small);\r
+ propHash.put("positive", positive);\r
+ propHash.put("negative", negative);\r
+ propHash.put("charged", charged);\r
+ propHash.put("aromatic", aromatic);\r
+ propHash.put("aliphatic", aliphatic);\r
+ propHash.put("tiny", tiny);\r
+ propHash.put("proline", proline);\r
+ propHash.put("polar", polar);\r
+ }\r
+\r
+ private ResidueProperties()\r
+ {\r
+ }\r
+\r
+ public static double getHydmax()\r
+ {\r
+ return hydmax;\r
+ }\r
+\r
+ public static double getHydmin()\r
+ {\r
+ return hydmin;\r
+ }\r
+\r
+ public static double[] getHyd()\r
+ {\r
+ return hyd;\r
+ }\r
+\r
+ public static Hashtable getAAHash()\r
+ {\r
+ return aaHash;\r
+ }\r
+\r
+ public static Hashtable getAA3Hash()\r
+ {\r
+ return aa3Hash;\r
+ }\r
+\r
+ public static int[][] getDNA()\r
+ {\r
+ return ResidueProperties.DNA;\r
+ }\r
+\r
+ public static int[][] getBLOSUM62()\r
+ {\r
+ return ResidueProperties.BLOSUM62;\r
+ }\r
+\r
+ public static int getPAM250(String A1, String A2)\r
+ {\r
+ Integer pog1 = (Integer) aaHash.get(A1);\r
+ Integer pog2 = (Integer) aaHash.get(A2);\r
+ int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];\r
+\r
+ return pog;\r
+ }\r
+\r
+ public static int getBLOSUM62(String A1, String A2)\r
+ {\r
+ int pog = 0;\r
+\r
+ try\r
+ {\r
+ Integer pog1 = (Integer) aaHash.get(A1);\r
+ Integer pog2 = (Integer) aaHash.get(A2);\r
+ pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ //System.out.println("Unknown residue in " + A1 + " " + A2);\r
+ }\r
+\r
+ return pog;\r
+ }\r
+\r
+ public static Vector getCodons(String res)\r
+ {\r
+ if (codonHash.containsKey(res))\r
+ {\r
+ return (Vector) codonHash.get(res);\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+ public static String codonTranslate(String codon)\r
+ {\r
+ Enumeration e = codonHash.keys();\r
+\r
+ while (e.hasMoreElements())\r
+ {\r
+ String key = (String) e.nextElement();\r
+ Vector tmp = (Vector) codonHash.get(key);\r
+\r
+ if (tmp.contains(codon.toUpperCase()))\r
+ {\r
+ return key;\r
+ }\r
+ }\r
+\r
+ return null;\r